Phytobiomes are compositionally nested from the ground up

Abstract

Plant-associated microbes are critical players in host health, fitness and productivity. Despite microbes’ importance in plants, seeds are mostly sterile, and most plant microbes are recruited from an environmental pool. Surprisingly little is known about the processes that govern how environmental microbes assemble on plants in nature. In this study we examine how bacteria are distributed across plant parts, and how these distributions interact with spatial gradients. We sequenced amplicons of bacteria from the surfaces of six plant parts and adjacent soil of Scaevola taccada, a common beach shrub, along a 60 km transect spanning O’ahu island’s windward coast, as well as within a single intensively-sampled site. Bacteria are more strongly partitioned by plant part as compared with location. Within S. taccada plants, microbial communities are highly nested: soil and rhizosphere communities contain much of the diversity found elsewhere, whereas reproductive parts fall at the bottom of the nestedness hierarchy. Nestedness patterns suggest either that microbes follow a source/sink gradient from the ground up, or else that assembly processes correlate with other traits, such as tissue persistence, that are vertically stratified. Our work shines light on the origins and determinants of plant-associated microbes across plant and landscape scales.

Natural Bacterial Assemblages in Arabidopsis thaliana Tissues Become More Distinguishable and Diverse during Host Development

“…However, studies of cultivated Agave have found that tissue explains more variation in community composition than species and site (27). Tissue type also explains more variation in epiphytic community composition than sample site in the species Scaevola taccada (28). Together, these results suggest that plants are best considered as collections of distinct habitat patches for bacterial colonization.…”

“…Recent evidence suggests that within plants, communities in different tissues are composed of a common pool of systemic colonists (24,25). However, individual lineages can display differences in colonization efficiency between roots and stems (26), and several studies have reported variation between the bacterial assemblages found in different tissues (27)(28)(29), supporting the idea that some bacteria are more successful than others in colonizing a given habitat within the plant. Variation in assemblage composition is also observed when plant tissues are sampled at different developmental stages (22,30,31).…”

Spatial and Structural Factors Shape Seagrass-Associated Bacterial Communities in Singapore and Peninsular Malaysia

“…Terrestrial plants show discrete microbial assemblages and communities dependent upon whether leaves, fruits, or roots are examined (Amend et al, 2019). Similarly, seagrass associated microbes occupy a number of distinct microenvironments across the plant (e.g., the phyllosphere, and the rhizosphere) (Hurtado-McCormick et al, 2019;Wainwright et al, 2019c).…”

Foliar mycoendophytome of an endemic plant of the Mediterranean biome (Myrtus communis) reveals the dominance of basidiomycete woody saprotrophs

“…This is clearly corroborated by not only the moderately high values of the network-level indexes of specialization (H2′) and checkerboard score (C-score), but also by the node-level indexes of node and normalized degree, and effective partners and proportional generality. Furthermore, as there was no association between the distance of the sampled trees and their corresponding foliar fungal endophytes community and the environmental conditions are quite the same in sampling area, tree distance most probably serves or as proxy for dispersal limitation or this pattern occurs due to priority effects, and, therefore, are stochastic environmental drivers (Amend et al, 2019) In spite of having worked with culture-dependent foliar endophytic fungal communities along with distinct North-American biomes, Chagnon et al (2016) approximately retrieved these same network-level patterns. Furthermore, Yao et al (2019) working on metabarcoding-analyzed endophytic fungal communities associated with the leaves of six mangrove species, observed that endophytic network structure was characterized by significantly highly specialized and modular but lowly connected and anti-nested properties.…”

“…This is clearly corroborated by not only the moderately high values of the network-level indexes of specialization (H2′) and checkerboard score (C-score), but also by the node-level indexes of node and normalized degree, and effective partners and proportional generality. Furthermore, as there was no association between the distance of the sampled trees and their corresponding foliar fungal endophytes community and the environmental conditions are quite the same in sampling area, tree distance most probably serves or as proxy for dispersal limitation or this pattern occurs due to priority effects, and, therefore, are stochastic environmental drivers ( Amend et al, 2019 )…”